Introduction to Biology: What is Science and Living Systems?

1. Outline of Lectures 1 and 2: • What is Biology? • What is Science? • Context: Ways of Knowing • What Distinguishes Living Systems?

2. I. What is Biology?

3. I. What is Biology? Webster’s New World Dictionary: "the science that deals with the origin, history, physical characteristics, life processes, habits, etc. of plants and animals: it includes botany and zoology."

4. I. What is Biology? Webster’s New World Dictionary: "the science that deals with the origin, history, physical characteristics, life processes, habits, etc. of plants and animals: it includes botany and zoology." The scientific study of living systems.

5. I. What is Biology? Webster’s New World Dictionary: "the science that deals with the origin, history, physical characteristics, life processes, habits, etc. of plants and animals: it includes botany and zoology." The scientific study of living systems. Begs two questions – “what is science?” and “What distinguishes living systems?”

6. II. What is Science? A. Definition: Webster’s: “systematized knowledge derived from observation, study, and experimentation carried on in order to determine the nature or principles of what is being studied. The systematized knowledge of nature and the physical world.”

7. II. What is Science? A. Definition: Webster’s: “systematized knowledge derived from observation, study, and experimentation carried on in order to determine the nature or principles of what is being studied. The systematized knowledge of nature and the physical world.”

8. II. What is Science? B. Limitations: - What is studied: the physical world /universe A medieval, Ptolemeic view of the universe

9. II. What is Science? B. Limitations: - What is studied: the physical world /universe - How it is studied (Method): empiricism “of the senses”, but not “common sense”…

10. Methodological Approaches: • 1. REDUCTIONISM • Gaining an understanding of a system by describing its subsystems (components)

11. Methodological Approaches: • 1. REDUCTIONISM • Gaining an understanding of a system by describing its subsystems (components) ≠ “emergent properties”

12. Powerful Approach: living systems are very complex, so describing the STRUCTURE can give insights into FUNCTION.

13. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • The function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems).

14. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • The function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems). How could a complex system like a camera eye, composed of mutually dependent parts, have evolved through a stepwise sequence? Half an eye (lens) can’t work…

15. 2. COMPARATIVE METHOD The function of complex systems may be understood by comparing them with simpler systems (with fewer subsystems). Visual systems in molluscs: Half an eye (retina) CAN work…

16. 2. COMPARATIVE METHOD Why is this method so powerful in biology? Is there a REASON why different organisms might have similar structures and functions?

17. 2. COMPARATIVE METHOD Why is this method so powerful in biology? Is there a REASON why different organisms might have similar structures and functions? Yes… common ancestry. This is why the use of model organisms (E. coli, fruit fly, house mouse) illuminates the field of medicine

18. And the most dramatic examples of homology are in the hoxgenes, as well. In fact, the homology is so good that lineages of eyeless flies lacking that hox gene can have the ability to grow eyes restored by adding the homologous gene from a mouse…and flies develop compound eyes with the mouse hox gene for eye development, even though mice have camera eyes… HOW COOL IS THAT!?

19. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • 3. EXPERIMENTATION (EMPIRICISM)

20. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • 3. EXPERIMENTATION (EMPIRICISM) Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, there are no spiders”

21. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: is this relationship causal? Bring other observed facts to bear “They use similar habitats” (could live together) “Lizards eat spiders” “Lizards and spiders eat other insects” “They disperse differently” (so they may have gotten to different islands by chance)

22. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: create a falsifiable (testable) causal hypothesis GOAL: is this relationship causal?

23. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: create a falsifiable (testable) causal hypothesis GOAL: is this relationship causal? Bring other observed facts to bear “They use similar habitats” (could live together) “Lizards eat spiders” “Lizards and spiders eat other insects” “They disperse differently” (so they may have gotten to different islands by chance) “Hawks eat lizards but not spiders, so maybe it just happens that hawks and spiders are together” “Some warblers eat spiders and not lizards, and maybe it just happens that warblers and lizards are together” “Lizards run around and may break spider webs and starve them inadvertently”

24. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: create a falsifiable (testable) causal hypothesis Bring other observed facts to bear “They use similar habitats” (could live together) “Lizards eat spiders” “Lizards and spiders eat other insects” “They disperse differently” (so they may have gotten to different islands by chance) “Hawks eat lizards but not spiders, so maybe it just happens that hawks and spiders are together” “Some warblers eat spiders and not lizards, and maybe it just happens that warblers and lizards are together” “Lizards run around and may break spider webs and starve them inadvertently”

25. You can envision many alternative causal hypotheses …and there are nearly a limitless supply…you can’t test them all (so scientific facts aren’t eternal truths or PROOFS)… test the simplest explanation first = “principle of parsimony” or “Occam’s razor” Bring other observed facts to bear “They use similar habitats” (could live together) “Lizards eat spiders” “Lizards and spiders eat other insects” “They disperse differently” (so they may have gotten to different islands by chance) “Hawks eat lizards but not spiders, so maybe it just happens that hawks and spiders are together” “Some warblers eat spiders and not lizards, and maybe it just happens that warblers and lizards are together” “Lizards run around and may break spider webs and starve them inadvertently”

26. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: create a falsifiable (testable) causal hypothesis GOAL: is this relationship causal? Other observations Hypothesis: Lizard predation causes a reduction in spider abundance on Caribbean Islands You have just used Inductive logic , using specific observations to formulate a general principle

27. Observerepeated, correlated physical phenomena/patterns “On Caribbean Islands with lizards, spiders are rare” GOAL: create a falsifiable (testable) causal hypothesis GOAL: is this relationship causal? Other observations Hypothesis: Lizard predation causes a reduction in spider abundance on Caribbean Islands. Alternative Hypothesis: Lizard predation does not cause a reduction in spider abundance… (maybe competition does or maybe it is just a correlated effect of something else…) Here is a another critical element of a scientific hypothesis – it must be falsifiable – you must be able to envision data collected from the physical universe that would prove your hypothesis is wrong.

28. Hypothesis: Lizard predation causes a reduction in spider abundance on Caribbean Islands Alternative Hypothesis: Lizard predation does not cause a reduction in spider abundance… (maybe competition does or maybe it is just a correlated effect of something else…) Conduct an experiment in which data supporting either hypothesis is possible.

29. To do this, you use deductive logic (general to specific case). IF my general principle (hypothesis) is true, THEN I can predict a specific outcome in my particular experiment. IF: - lizard predation is responsible for low spider abundance And IF: - I add lizards to specific islands and remove lizards from others, with appropriate controls for the manipulations, THEN: - Spider abundance should decline where I add lizards and increase where I remove lizards, and spiders should be a major component of lizard diets (gut content analysis).

30. IF: - lizard predation is responsible for low spider abundance And IF: - I add lizards to specific islands and remove lizards from others, with appropriate controls for the manipulations, THEN: - Spider abundance should decline where I add lizards and increase where I remove lizards, and spiders should be a major component of lizard diets (gut content analysis). Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works. (Usually by statistical inference…which we will demonstrate in lab…)

31. Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works. Many lines of independent evidence…

32. Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works. Many lines of independent evidence… can support a single general explanation

33. Then you do it and see!!! And you generalize from your specific experiment to nature (inductive logic). You use logic and evidence from the physical world to reach a conclusion about how nature is and how it works. Many lines of independent evidence… can support a single general explanation… These Explanations are THEORIES. They are supported by experimental results and they can be tested by subsequent experiments

34. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • 3. EXPERIMENTATION (EMPIRICISM) • 4. METHODOLOGICAL MATERIALISM

35. Methodological Approaches: • 1. REDUCTIONISM • 2. COMPARATIVE METHOD • 3. EXPERIMENTATION (EMPIRICISM) • 4. METHODOLOGICAL MATERIALISM • Philosophical materialism – the material is all there is. • Methodological materialism – the material is all we can test.

36. II. What is Science? A. Definitions B. Limitations C. Theories - tested, explanatory models of how the physical universe works

37. II. What is Science? A. Definitions B. Limitations C. Theories - tested, explanatory models of how the physical universe works Chemistry: “Chemical Bond Theory” Physics: “Atomic Theory” Astronomy: “Heliocentric Theory” Biology: “Evolutionary Theory”

38. III. Context: Ways of Knowing A. Why You Know - Searching for Truth 1. Faith: Webster’s – “unquestioning belief not requiring proof or evidence”

39. III. Context: Ways of Knowing • A. Why You Know - Searching for Truth • Faith: Webster’s – “unquestioning belief not requiring proof or evidence” • Logic: “the science of correct reasoning; science which describes relationships among propositions in terms of implication, contradiction, contrariety, conversion, etc.” Evidence is a "clean argument“, but it does not have to describe a physical reality.

40. III. Context: Ways of Knowing • A. Why You Know - Searching for Truth • Faith: Webster’s – “unquestioning belief not requiring proof or evidence” • Logic: “the science of correct reasoning; science which describes relationships among propositions in terms of implication, contradiction, contrariety, conversion, etc.” Evidence is a "clean argument“ • Science: Logical argument and physical evidence.

41. III. Context: Ways of Knowing A. Why You Know - Searching for Truth B. Different Problems, Different Tools “If the only tool you have is a hammer, you tend to see every problem as a nail.” – Abraham Maslow, American Psychologist Is abortion right? How old is the Earth?

42. I. What is Biology? Begs two questions – “what is science?” and “What distinguishes living systems?” II. What is Science? III. Ways of Knowing IV. What Distinguishes Living Systems?

43. IV. What Distinguishes Living Systems? • Characteristics • 1. O__ • 2. R__ • 3. R__ • 4. G__ • 5. E__ • 6. E__

44. IV. What Distinguishes Living Systems? • Characteristics • 1. Ordered Organization – highly complex and non-random systems requiring energy input for their maintenance. They are open systems that can achieve greater order by an input of more energy or greater efficiency.

45. IV. What Distinguishes Living Systems? • Characteristics • 1. Ordered Organization – highly complex and non-random systems requiring energy input for their maintenance. They are open systems that can achieve greater order by an input of more energy or greater efficiency. • - highly organized at different spatial and temporal scales

46. Spatial Scales: • Biosphere: Earth is ~4 x 107 m in circumference • Ecosystem: drop of pondwater (1 x 10-3 m) to Amazon Rain Forest (5 x 106 m). • Community: equally variable • Population: equally variable • Individual: Smallest Mammal - Pygmy Shrew: 2 inches (5 x 10-2 m) • Largest Animal Ever - Blue Whale: 100 feet (3 x 101 m) • Human - 6 ft... 2 x 100 m • Largest Organism: Fungus covering 37 acres (7 x 102 m) • Organs: variable • Cells: Liver Cell: 2 x 10-5 m (2/100ths of a mm) • E. coli Bacterium: 2 x 10-6 (1/10th of a liver cell) • Virus: 2.5 x 10-8 (1/100th of a bacterium) • Organelles: Ribosome: 1.8 x 10-8 m • Mitochondrion: 2.5 x 10-6 m (about bacteria sized) • Molecules: Hemoglobin (average protein): 6.8 x 10-9 m (1/1000th of a bact.) Phospholipid: 3.5 x 10-9 m • Amino Acid: 5.0 x 10-10 m • Atoms: Carbon: 1 x 10-10 m (1/10,000,000,000 m - a ten billionth of a meter) (a ten millionth of a millimeter) • (a ten thousandth the length of a liver cell) • 11. Nucleus: 2 x 10-15 m. 5 orders of magnitude smaller than the width of the atom!!!

47. So, the nucleus is only 1/50,000th the width of the atom. Atoms are mostly space… matter is mostly space… In fact, a cubic centimeter of nuclear matter (no space) would weigh 230 million tons (Physics by J. Orear, 1979) Analogy: If a basketball 1 ft. in diameter represents the nucleus of an atom, the edge of the electron cloud would be about 5 miles away in either direction; the atom would be 10 miles wide (~ 50,000 ft.)… that’s a lot of empty space. Analogy: You and the Earth are separated by 7 orders of linear magnitude. A millimeter (about the size of a bold-faced period) and a carbon atom are separated by 7 orders of linear magnitude. So, to a carbon atom, the period is it's Earth.... mind blowing... Cells make up living systems that can be 12 orders of magnitude larger (cell to biosphere).

48. B. Temporal Scales: 1. Age of Earth: 4.5 x 109 yrs (4.5 billion) 2. History of Life on Earth: 3.5 x 109 years 3. Oldest Eukaryotic Cells: 1.8 x 109 years 4. Oldest Multicellular Animals: 6.1 x 108 years 5. Oldest Vertebrates: 5.0 x 108 (500 million) 6. Oldest Land Vertebrates: 3.6 x 108 7. Age of Dinosaurs - Mesozoic: 240-65 million 8. Oldest Primates: 2.5 x 107 (25 million) 9. Oldest Hominids: 4.0 x 106 (4 million – 1/1000th of earth history) 10. Oldest Homo sapiens: 2.0 x 105 (200,000) 11. Oldest Art: 3.0 x 104 (30,000; 1/100,000th of Life's History) 12. Oldest Agriculture: 1.0 x 104 (10,000) 13. Oldest Organism: Bristlecone pines: 5 x 103 14. Human cell: brain/muscle 70 yrs Red Blood Cell - weeks Skin cell – days 15. Supply of ATP in cell - 2 seconds 16. Rates of chemical reactions - milliseconds (3.1 x 10-10 ms/year). The history of life, spanning billions of years, is dependent on reactions that occur at a temporal scale separated by 19 orders of temporal magnitude.

49. IV. What Distinguishes Living Systems? • Characteristics • 1. Order • 2. Reproduction: • asexual/clonal/fragmentation • sexual: production of new genome • Inexact reproduction (through mutation and sex) creates hierarchical patterns of relatedness among organisms over time: • genealogies and phylogenies

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